DPCfam Metaclusters

🧬 Domain Classification in Sequence Space
DPCfam Standard DPCfam DPCfamB

The DPCfam pipeline applied the Density Peak Clustering (DPC) algorithm to roughly 23 million UniRef50 sequences (UniRef50 v. 2017_07) and automatically grouped homologous domain segments into 81,384 protein families called metaclusters, entirely without manual curation. Each metacluster was then used to build a multiple sequence alignment and a profile-HMM for downstream analysis.

The table below lists all 81,384 DPCfam metaclusters by default. Use the toggle buttons above to switch to the Standard subset (size ≥ 50 seeds, 46,828 metaclusters) or the DPCfamB subset (25 to 49 seeds, 34,556 metaclusters). Intrinsic metacluster properties appear on the left; Pfam annotations on the right. Click any MCID to open its detail page.

MCID Size UniRef50 Avg. Len. Std avg len % LC % CC % DIS Avg. TM Pfam DA % DA % Avg. Ov. Overlap Label
MC451706 44 324.18 39.28 0.22 0.0 66.69 0.0 PF01602 2.63 5.49 Shifted
MC451731 39 152.95 25.44 0.03 0.0 0.23 1.5 PF00487 66.67 50.66 Reduced
MC451735 42 58.38 12.46 0.02 0.0 16.6 0.0 PF04616 64.86 11.28 Shifted
MC451739 33 110.7 20.05 0.41 0.0 0.66 2.67 UNKNOWN 0.0 0.0 NONE
MC451749 26 176.73 18.18 0.03 0.0 3.74 0.0 PF10139 100.0 26.15 Reduced
MC451780 27 322.18 35.48 0.03 0.0 4.15 0.06 UNKNOWN 0.0 0.0 NONE
MC451856 42 84.26 6.21 0.04 0.0 20.07 0.0 PF09793 96.97 33.96 Shifted
MC451859 31 344.68 16.85 0.1 0.0 0.41 0.12 PF12530 100.0 74.04 Extended
MC451867 30 76.27 15.86 0.02 0.0 2.01 0.0 UNKNOWN 0.0 0.0 NONE
MC451877 46 57.96 8.96 0.02 0.0 0.79 0.0 PF02221 92.5 53.37 Reduced
Legend
  • A. Metacluster Intrinsic Properties:
  • MCID: Unique identifier per metacluster.
  • 1. Size UniRef50 : Number of UniRef50 seed sequences in the metacluster.
  • 2. Avg. Len.: Mean domain length of the seeds (in amino acids).
  • 3. Std. Avg. Len.: Standard deviation of seed domain lengths.
  • 4. % LC Percent of residues located in low-complexity regions.
  • 5. % CC: Percent of residues located in coiled-coil regions.
  • 6. % DIS: Percent of residues predicted as intrinsically disordered.
  • 7. Avg.TM: Average number of transmembrane regions per domain.
  • B. Pfam Annotations:
  • 1. Pfam DA: Pfam architecture which best overlaps with MC. We refer to it as the dominant architecture (DA). If there is no overlap, the MC is tagged as UNKNOWN (representing 'dark matter').
  • 2. % DA: Percent of sequences in the MC matching the DA.
  • 3. % Avg. Ov.: Average % boundary overlap between the MC and Pfam, computed only for seeds that match the DA.
  • 4. Overlap Label: Label describing qualitatively the overlap of the MC with its DA, which can be : equivalent, reduced, extended or shifted. NONE, otherwise.
    Color-coded based on boundary agreement:
    • Yellow (Equivalent): the MC and its dominant architecture share very similar boundaries.
    • Blue (Reduced): the MC covers only part of the dominant architecture.
    • Pink (Extended): the MC extends beyond the dominant architecture boundaries.
    • Green (Shifted): the MC and the dominant architecture share a boundary offset, with poor positional agreement.